Biology subjects

Karmakar, T.

Publications and source records attributed to Karmakar, T..

4 recordsLinked to original sources

bioRxiv2025

Understanding RNA Chaperone Activity of ProQ Protein

RNA-binding proteins (RBPs) are crucial in recognizing and binding small RNAs that modulate gene expression. RBPs often act as RNA chaperones, facilitating the sRNA-mRNA duplex formation. One of the most studied sRNA chaperones is Hfq, the post-transcriptional gene regulator in bacteria. Recently, a new RNA-chaperone protein, ProQ, has been discovered, which binds to a novel sRNA RaiZ, derived from the 3-end of mRNA encoding ribosome-inactivating protein, and promotes its base pairing with the ribosome binding site of hupA mRNA, leading to the repression of HU- protein synthesis. Despite these studies, the RNA-binding mechanism in ProQ has not been well explored in detail to date. In this work, we studied the binding of raiZ RNA to ProQ using atomistic long-timescale molecular dynamics and on-the-fly probability-based enhanced sampling (OPES) simulations. The raiZ RNA binds to ProQs concave surface, mostly decorated with polar and positively charged residues like Arginine and Lysine, exerting electrostatic stabilization to the RNA. In-silico mutations of these crucial residues lead to a significant loss of the intermolecular interactions, resulting in the detachment of the RNA from the protein. The free energy surface obtained from the OPES simulation helps identify stable raiZ-bound ProQ structures as well as intermediate states. The pertinent atomistic insights into the protein-RNA interactions and deciphering the binding mechanism of the raiZ RNA to ProQ enrich our knowledge about ProQ and its RNA chaperone activity.

biophysics↗

bioRxiv2024

Enhanced Sampling Simulations of RNA-peptide Binding using Deep Learning Collective Variables

Enhanced sampling (ES) simulations of biomolecular recognition such as binding of small molecules to proteins and nucleic acids targets, protein-protein association, and protein-nucleic acids interactions have been gaining significant attention in the simulation community due to their ability to sample long timescale processes. However, a key challenge in implementing collective variable (CV)-based enhanced sampling methods is the selection of appropriate CVs that can distinguish the systems metastable states and, when biased, can effectively sample these states. This challenge is particularly acute when simulating the binding of a flexible molecule to a conformationally rich host molecule, such as the binding of a peptide to an RNA. In such cases, a large number of CVs are required to capture the conformations of both the host and the guest, as well as the binding process. In our work, we employed the recently developed Deep Targeted Discrimination Analysis (DeepTDA) method to design CVs for the study of the binding of a cyclic peptide, L22 to a TAR RNA of HIV as a prototypical system. These CVs were used in the on-the-fly probability-based enhanced sampling and well-tempered metadynamics simulations to sample reversible binding and unbinding of L22 peptide to the TAR RNA target. The enhanced sampling simulations revealed multiple binding and unbinding events, which enabled the calculation of the free energy surface for the peptide binding process. Our results demonstrate the potential of the DeepTDA method for designing CVs to study complex biomolecular recognition processes.

biophysics↗

bioRxiv2022

Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters

Monolayer-protected atomically precise metal nanoclusters (MPC) are an important class of molecules that have potential applications in catalysis, imaging, and drug delivery. Recent studies have shown that peptide-based drugs can be complexed with MPCs to avoid enzymatic degradation and get delivered to targeted cells. Although the MPCs potential role in imaging and drug delivery processes have been studied, for their impactful use, specific molecular interactions between MPCs and biomolecules, mainly proteins and peptides should be explored in detail. In this work, we have carried out atomistic molecular dynamics simulations to investigate the interactions between Au-based MPCs and an anticancer peptide, melittin. The MEL peptides get attached to the MPCs surface by the formation of multiple hydrogen bonds between the peptide amino acid residues with MPCs ligands. Additionally, the positively charged residues such as Lys and Arg, the Trp, and the N-terminal of the peptide anchor strongly to the MPC core playing a crucial role in the peptides overall stabilization on the MPC surface.

biophysics↗

bioRxiv2021

Structural basis for the hyperthermostability of an archaeal glutaminase induced by post-translational succinimide formation

Stability of proteins from hyperthermophiles enabled by reduction of conformational flexibility is realized through various mechanisms. Presence of a stable, hydrolysis-resistant succinimide arising from cyclization of the side chains of aspartyl/asparaginyl residues with backbone amide -NH of the succeeding residue would restrain the torsion angle {Psi}. Here, we describe the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase (MjGATase) and address the mechanism of a succinimide-induced increased thermostability using molecular dynamics simulations. This study reveals the interplay of negatively charged electrostatic shield and n[->]{pi}* interactions in preventing succinimide hydrolysis. The stable succinimidyl residue induces formation of a conformational-lock, reducing protein flexibility. Protein destabilization upon replacement with the {Phi}-restricted prolyl residue highlights the specificity of the conformationally restrained succinimidyl residue in imparting hyperthermostability. The conservation of succinimide-forming tripeptide sequence (E(N/D)(E/D)) in a group of archaeal GATases suggests an adaptation of this otherwise detrimental post-translational modification as an inducer of thermostability.

biochemistry↗